class CircosConfigParser:
'''
circos implemented the apache config format which has no builtin parser in python. this class is intended to parse and manipulate the circos configuration files.
'''
def __init__(self, configType):
self.configType = configType
self.xmlParser=None
self.txtParser=None
self.conf_file= file_provider['circos_config'][configType]
self.parse()
def parse(self):
'''
returns a tuple with the first item as a dictionary of attributes outside xml blocks AND the second item as a list of xml blocks. the first item is straight forward. Second item should be further parsed iteratively by using the iPaseXML function
'''
with open(self.conf_file) as f:
text=f.read()
self.xmlParser= MyXMLParser(text)
xml_text= self.xmlParser.tostring()
non_xml_text= text.replace(xml_text, "")
self.txtParser= SettingParser(non_xml_text)
def set(self, prop, value, item_tag="", refProp="index", refValue= ""):
if item_tag != "": ## means coming from the xml part
self.xmlParser.set(item_tag, prop, value, refProp, refValue)
else: ### means coming from the text part
self.txtParser.set(prop, value)
self.write()
def write(self):
### !!! TODO: this part should be rewritten
### There is still a problem with the xmlparser.
with open(self.conf_file,'w') as f:
f.write(self.tostring())
def tostring(self):
if self.configType == 'plots':
self.doc= self.xmlParser.tostring()
else:
self.doc= self.txtParser.tostring() + self.xmlParser.tostring()
return self.doc
def parse(self):
'''
returns a tuple with the first item as a dictionary of attributes outside xml blocks AND the second item as a list of xml blocks. the first item is straight forward. Second item should be further parsed iteratively by using the iPaseXML function
'''
with open(self.conf_file) as f:
text=f.read()
self.xmlParser= MyXMLParser(text)
xml_text= self.xmlParser.tostring()
non_xml_text= text.replace(xml_text, "")
self.txtParser= SettingParser(non_xml_text)